85-year-old Advani, a founder member of BJP, had first resigned as party president on June 7, 2005 following widespread criticism from the Rashtriya Swayamsevak Sangh and right wing outwits over his remarks praising Jinnah during his six-day visit to Pakistan. Advani had described Jinnah as a "secular" leader.
Advani, whose trip to Pakistan was seen as an attempt to reposition himself politically and to shed the hardline tag and recast himself as a moderate more palatable to a wider electorate, had spoken of Jinnah's "forceful espousal of a secular state in which every citizen would be free to practice his own religion".
He had described Jinnah as one of the "very few who actually create history".
Advani, however, withdrew his resignation from the party chief's post after intense parleys, ending a four-day long leadership crisis in the opposition party.
Despite the resolution of the crisis, ties remained strained between Advani and the RSS, the party's fountainhead.
Less than seven months after he withdrew his resignation, Advani stepped down as party president on December 31, 2005 bringing to an end the controversy triggered by his praise of Jinnah. He was succeeded by the current party president Rajnath Singh.
The formal resolution of the crisis in June took place at a meeting of the BJP parliamentary board and central office-bearers to which the chief ministers of BJP-ruled states were also invited.
A one-page resolution adopted at the meeting to which Advani was also a party blamed Jinnah for the partition and the violence that followed.
All the BJP leaders stood together on the issue of "no deviation from ideology" and went along with the RSS position that there could be no question of re-evaluating Jinnah or his role in Partition.
The BJP veteran, who was appointed president in October 2004, stood by his comments while sending in his resignation lettter. It was Advani's third term as BJP chief.
"I have not said or done anything in Pakistan which I need to retract or review", Advani wrote in a letter in which he requested the BJP to "relieve" him of his post.
RSS and the Vishwa Hindu Parishad demanded to know why Advani had "heaped praise" on Jinnah.
Advani had also drawn criticism from the ruling Congress.
"It is truly ironic and astounding that Mr Advani considers Mr Jinnah secular. Perhaps he would like to explain to the nation the new definition of secularism," Congress spokesman Abhishek Singhvi had said.
Advani announced his resignation for the second time at a press conference, a day after the BJP's silver jubilee National Council session concluded in Mumbai.
He had denied that he was forced to resign under the pressure of RSS. He said he had acted on his declaration at the Chennai national executive session in September.
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